JMP Genomics processes require that missing
genotypes
be represented using specific formats.
Recode Missing Genotypes
creates a modified data set in which nonstandard formats used to represent missing genotypes or
alleles
are replaced with the specific values required by the Genetics processes: blank ( ) for character genotypes or alleles and a period (.) for numeric genotypes or alleles.
One
Input Data Set
, containing the marker data is required to run the
Recode Missing Genotypes
process. The
samplegmdata_missgeno_a.sas7bdat
data set used in the following example represents a modification of the
computer-generated
samplegmdata.sas7bdat
data set
described in
Data Sets Used in JMP Genomics Processes
.
This data set
consists of 1000 rows of individuals with 60 columns corresponding to data on these individuals. Marker data is presented in the one-column format. This data set is partially shown below. Note that this is a wide data set; markers are listed in columns, whereas individuals are listed in rows. Missing genotypes, such as the one that is circled, are represented with an asterisk (*).
This data set is included in the
Sample Data
folder.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
Output from this process is accessed from a
Results
window. Refer to the
Recode Missing Genotypes
output documentation for detailed descriptions and guides to interpreting your results.